Redesign of iPPI-DB, a database for modulators of Protein-Protein Interactions

Rachel Torchet (1) , Alexandra Moine-Franel (1, 2) , Hélène Borges (1, 2) , Bryan Brancotte (1) , Olivia Doppelt-Azeroual (1) , Fabien Mareuil (1) , Hervé Ménager (1) , Olivier Sperandio (1, 2)

1 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
2 Bioinformatique structurale - Structural Bioinformatics

iPPI-DB, for inhibitors of Protein-Protein Interaction DataBase, is a web application first released in 2012, which stores physicochemical and pharmacological data about PPI modulators and their targets. Users can query the database using either pharmacological criteria or chemical similarity with a user-defined query compound. The database is manually curated from the scientific literature and contains more than a thousand non-peptide inhibitors (iPPI) across 18 families of Protein-Protein Interactions. In the initial version, The chemical structures, as well as the physicochemical and the pharmacological profiles of these compounds and their targets, were extracted from the literature, computed and retrieved using numerous manual steps. This rather tedious procedure was seriously hindering the updates of the database. For this project, we applied a combination of Agile methods and a User-Centered Design (UCD) approach to completely redesign the iPPI-DB web application. The main goal of this redesign is to focus on the needs of the user, ensuring that the end product fits the purpose, increasing the number of entries in the database and easing the query process. We adopted an iterative approach, interleaving successive series of design, tests and implementation steps, involving users in each iteration. This process, although it required an important involvement from the users during the project, has been extremely beneficial, as it allowed us to build a constructive dialog between scientists and the development team, and quickly validate or ask for corrections in the software. The resulting web application provides a rich, robust, and innovative software environment to facilitate the growth and the maintenance of the database, and to query it using a highly intuitive and extremely powerful user interface

Keywords: Web interface; Database; UX Design; Protein-Protein interaction

Domains: Bioinformatics [q-bio.QM]

Rachel Torchet, Alexandra Moine-Franel, Hélène Borges, Bryan Brancotte, Olivia Doppelt-Azeroual, et al.. Redesign of iPPI-DB, a database for modulators of Protein-Protein Interactions. JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques), Société Française de BioInformatique; GdR Bioinformatique Moléculaire; Institut Francais de Bioinformatique, Jul 2019, Nantes, France. ⟨pasteur-02867265⟩